In December 2016, ED registered a criminal case against Naik for money laundering following a complaint by the National Investigation Agency under the Unlawful Activities (Prevention) Act.

According to Hiten Venegaonkar, ED's lawyer, Naik tried to lay down conditions for appearance before the court. Besides demanding the agency for more time, he even asked them to record his statement through a video link, the lawyer claimed.

According to Zee News, Venegaonkar said, "Under section 15 of Prevention of Money Laundering Act (PMLA), a person against whom summons is issued has to appear before the agency in person to record his or her statement."

According to an email sent to the ED, Naik said, "I have done nothing ever that is outside the framework of law or contrary to what the law of land stipulates. As currently I am not in the country it is taking a substantial effort on the part of my people to collate all the related data to be given to you."

However, the agency has taken the statements of Aamir Gazdar, an employee of Naik's institute, Islamic Research Foundation and Naik's sister, Nailah Naushad Noorani, to prove he was laundering money using the charitable organisation as a front.